June 03, 2013

Dog domestication parameters from full genome sequencing

This paper casts doubt on the dominant scenario about the Southeast Asian geographical origin of dogs, while at the same time affirming their monophyletic origin and late pre-Neolithic domestication. The authors also document traits that were under selection during domestication.

It would be interesting to know what kinds of roles early dogs. Presumably early pre-Neolithic dogs functioned more as hunting companions, while those of Neolithic societies also had an increasing role as guards -since there was then property that needed guarding. How do modern dog breeds differ genetically to accommodate these roles, and might we one day figure out the original tasks of "multi-purpose" animals such as dogs?

arXiv:1305.7390 [q-bio.GN]

Genome Sequencing Highlights Genes Under Selection and the Dynamic Early History of Dogs

Adam H. Freedman et al.

To identify genetic changes underlying dog domestication and reconstruct their early evolutionary history, we analyzed novel high-quality genome sequences of three gray wolves, one from each of three putative centers of dog domestication, two ancient dog lineages (Basenji and Dingo) and a golden jackal as an outgroup. We find dogs and wolves diverged through a dynamic process involving population bottlenecks in both lineages and post-divergence gene flow, which confounds previous inferences of dog origins. In dogs, the domestication bottleneck was severe involving a 17 to 49-fold reduction in population size, a much stronger bottleneck than estimated previously from less intensive sequencing efforts. A sharp bottleneck in wolves occurred soon after their divergence from dogs, implying that the pool of diversity from which dogs arose was far larger than represented by modern wolf populations. Conditional on mutation rate, we narrow the plausible range for the date of initial dog domestication to an interval from 11 to 16 thousand years ago. This period predates the rise of agriculture, implying that the earliest dogs arose alongside hunter-gathers rather than agriculturists. Regarding the geographic origin of dogs, we find that surprisingly, none of the extant wolf lineages from putative domestication centers are more closely related to dogs, and the sampled wolves instead form a sister monophyletic clade. This result, in combination with our finding of dog-wolf admixture during the process of domestication, suggests a re-evaluation of past hypotheses of dog origin is necessary. Finally, we also detect signatures of selection, including evidence for selection on genes implicated in morphology, metabolism, and neural development. Uniquely, we find support for selective sweeps at regulatory sites suggesting gene regulatory changes played a critical role in dog domestication.

At least for me, there is sufficient evidence that dogs are 2-3 times as old. It is also much, much more plausible that the dog bottleneck corresponds to the ice age, and not to the introduction of agriculture. I very much doubt that all lineages except one died out post-LGM, and I also doubt such dogs then spread world-wide within a few thousand years.

Also, both the Basenji and Dingo are not particularly "ancient" lineages - if anything, they have undergone their own idiosyncratic bottlenecks and re-expansions, which does not make them particular useful for a study like this. There is a lot wider gene pool out there to study. As I have mentioned in the past, in addition to major lines that are known not to be too inbred and Siberian & Alaskan dogs, I would look at dogs in remote villages of Central, South and West Asia and even (e.g., East-Central and NE) Europe, in locations where people would have been least likely to purchase or raise expensive new breeds or would not have cared for particular breeds as long as the local dogs did their job. There may also be surprises in places like the central Amazon or the southern Andes.

Wolves have a tail gland, dogs don't, but the Ridgeback has a whorl/ridge on its back to its tail which appears related; Ridgeback pups with exposed "cysts" tend to get infected and die young (possibly used as food source by AMH human settlers on Phu Quoc island, Vietnam, while healthy pups were tamed & trained for hunting/guarding/carrying-pulling). All other dogs derived from the small Phu Quoc Ridgeback population, mixing with wolves for thick fur & pack hunt traits.

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